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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pynapple Resource Report Resource Website |
Pynapple (RRID:SCR_023312) | data analysis software, data processing software, software application, software resource, software toolkit, standalone software | Software object oriented, lightweight and standalone Python toolbox for neural data analysis. Its core features five versatile timeseries objects from Pandas library, allowing it the versatility to be used with most raw neuroscience data types and produce some common analysis forms. | OpenBehavior, neural data analysis, neuroscience data analysis, Pandas library objects, raw neuroscience data types, | is listed by: OpenBehavior | DOI:10.1101/2022.12.06.519376 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/pynapple/ | SCR_023312 | SciCrunch Registry | 2026-10-31 12:18:51 | 0 | ||||||||
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tmilltracker Resource Report Resource Website |
tmilltracker (RRID:SCR_023511) | software resource | Open source computer vision controlled treadmill system for small running animals such as insects and mice. Treadmill is controlled by Python software, allowing for flexible control of video tracking parameters, behavioral triggers, distance ran, and feedback. Used for studying locomotor behavior. | OpenBehavior, treadmill system, running animals, locomotor behavior, video tracking parameters, behavioral triggers, distance ran, | is listed by: OpenBehavior | BBSRC Research Experience Placement ; Nuffield Foundation Science Bursary Programme ; Royal Society Research |
DOI:10.1016/j.jneumeth.2013.03.009 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/tmilltracker/ | SCR_023511 | SciCrunch Registry | 2026-10-31 12:18:51 | 0 | |||||||
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Automated 2 Photon Imaging Compatible Platform for Assessing Working Memory Resource Report Resource Website |
Automated 2 Photon Imaging Compatible Platform for Assessing Working Memory (RRID:SCR_023463) | instrument resource | Open source automated platform for assessing working memory and prefrontal circuit function. Designed for automated, high-throughput assessments of working memory and simultaneous two-photon imaging in chronic stress studies. Physiology compatible behavioral platform designed specifically for studying circuit mechanisms underlying working memory and related cognitive functions in chronic stress states. | OpenBehavior, instrument, assessing working memory, prefrontal circuit function, chronic stress, behavioral platform, | is listed by: OpenBehavior | DOI:10.1016/j.ynstr.2023.100518 | SCR_023463 | SciCrunch Registry | Automated 2-Photon Imaging-Compatible Platform for Assessing Working Memory | 2026-10-31 12:18:51 | 0 | |||||||||
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3D Printed Multi Pump System Resource Report Resource Website |
3D Printed Multi Pump System (RRID:SCR_023575) | instrument resource | System includes 3D Printed Syringe Pump Rack composed by 5 Syringe Pumps to have 2 continuous flow systems and one remaining pump. Syringe Pump is used to gradually administer small amounts of fluid to patient or for use in chemical and biomedical research. Main features include Open hardware/software, Extremely compact size ( 7cm movement range ), High precision lead screw and nut, Simple to use (command line interface), Simple to replicate, Minimal clean Design. | 3D Printed Syringe Pump Rack, Syringe Pumps, continuous flow system, OpenBehavior | is listed by: OpenBehavior | Freely available, Available for download, | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_023575.pdf | https://edspace.american.edu/openbehavior/project/3d-printed-multi-pump-system/ | SCR_023575 | SciCrunch Registry | 3D Printed Syringe Pump Rack | 2026-10-31 12:18:53 | 0 | |||||||
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RatHeadphones Resource Report Resource Website |
RatHeadphones (RRID:SCR_023667) | software resource | Repository for highly controlled sound presentation in freely moving rats. Provides all necessary information for building, adjusting, and using Ratphones to reliably present auditory stimulation to freely moving rats. Used for 3D printing of headphones designed for auditory psychophysics in behaving rats. | OpenBehavior, instrument, highly controlled sound presentation, freely moving rats, auditory stimulation, 3D headphones printing, auditory psychophysics, behaving rats, | is listed by: OpenBehavior | Champalimaud Foundation ; EU FP7 Grant ; Human Frontier Science Program ; Marie Curie Career Integration Grant |
DOI:10.1523/ENEURO.0028-23.2023 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/ratphones/ | SCR_023667 | SciCrunch Registry | Ratphones | 2026-10-31 12:18:53 | 0 | ||||||
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Live Mouse Tracker Toolkit Analysis Resource Report Resource Website |
Live Mouse Tracker Toolkit Analysis (RRID:SCR_024592) | LMT Toolkit | software resource, web application | Open source web application created to analyze Live Mouse Tracker data easily and intuitively. Used to check reliability and to make some analysis of data from Live Mouse Tracker experiments. LMT stores data in SQLite files that requires some computer skills, but LMT-toolkit makes it easy to compute and extract behavioral profiles for each animal tested following step-by-step process. | OpenBehavior, check LMT data reliability, analyze Live Mouse Tracker data, compute and extract behavioral profiles, |
is listed by: OpenBehavior is related to: Live Mouse Tracker analysis is related to: Live Mouse Tracker project |
Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/live-mouse-tracker/ | SCR_024592 | SciCrunch Registry | , LMT Toolkit, lmt toolkit analysis, LMT toolkit analysis, LMT-toolkit, LMT-Toolkit Analysis, Live Mouse Tracker Toolkit | 2026-10-31 12:19:04 | 0 | |||||||
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Spike Forest project Resource Report Resource Website |
Spike Forest project (RRID:SCR_021472) | data or information resource, portal, project portal | Project related to neural data analysis. Provides open-source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website. | Validating automated neural spike sorters, electrophysiological recordings, spike sorting codes, spike sorting analysis, OpenBehavior |
is listed by: OpenBehavior is related to: Spike Forest |
DOI:10.7554/elife.55167 | Free, Freely available | SCR_021472 | SciCrunch Registry | Spike Forest | 2026-10-31 12:19:27 | 0 | ||||||||
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Pypreclin project Resource Report Resource Website |
Pypreclin project (RRID:SCR_021473) | data or information resource, portal, project portal | Project related to preprocessing of images. Provieds software Python tool to processes raw macaque fMRI images using algorithms embedded in automatic pipeline. | Raw macaque fMRI images, fMRI images, macaque images, Python, OpenBehavior |
is listed by: OpenBehavior is related to: Pypreclin |
DOI:10.1016/j.neuroimage.2019.116353 | Free, Freely available | SCR_021473 | SciCrunch Registry | Pypreclin | 2026-10-31 12:19:27 | 0 | ||||||||
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MNE Scan project Resource Report Resource Website |
MNE Scan project (RRID:SCR_021470) | data or information resource, portal, project portal | Project related to real time acquisition and processing of electrophysiological data.Provides software tool for acquisition and processing of electrophysiological data. | Electrophysiological data processing, medical regulatory requirements, build standalone applications, MEG data acquisition, MEG data processing, EEG data acquisition, MEG data acquisition, OpenBehavior |
is listed by: OpenBehavior is related to: MNE Scan |
DOI:10.1016/j.jneumeth.2018.03.020 | Free, Freely available | SCR_021470 | SciCrunch Registry | MNE Scan | 2026-10-31 12:19:28 | 0 | ||||||||
|
Live Mouse Tracker analysis Resource Report Resource Website 1+ mentions |
Live Mouse Tracker analysis (RRID:SCR_021505) | LMT analysis | software resource, software toolkit | Software package for Live Mouse Tracker analysis. lmt-analysis provides all analysis tools needed to extract information from tracking performed by live mouse tracker. | Live Mouse Tracker, Live Mouse Tracker data analysis, OpenBehavior |
is listed by: OpenBehavior is related to: Live Mouse Tracker project is related to: Live Mouse Tracker Toolkit Analysis |
PMID:31110290 | Free, Available for download, Freely Available | https://edspace.american.edu/openbehavior/project/live-mouse-tracker/ | SCR_021505 | SciCrunch Registry | , lmt-analysis, live mouse tracker analysis, LMT analysis | 2026-10-31 12:19:27 | 3 | ||||||
|
3DTracker project Resource Report Resource Website |
3DTracker project (RRID:SCR_021440) | data or information resource, portal, project portal | Project related to markerless computerized behavioral analysis for laboratory animals.Provides open source 3D video based behavioral analysis system for neuroscience. System includes open source software tool for 3D-video based markerless computerized behavioral analysis. | 3D video, computerized behavioral analysis, laboratory animals, reconstruct 3D image, animal image, 3D image, estimate animal 3D pose, behavior measurement, freely moving, head fixed, OpenBehavior |
is listed by: OpenBehavior is related to: 3DTracker |
Free, Freely available | SCR_021440 | SciCrunch Registry | 3DTracker | 2026-10-31 12:19:27 | 0 | |||||||||
|
LinCoM project Resource Report Resource Website |
LinCoM project (RRID:SCR_021438) | data or information resource, portal, project portal | Project related to animal behavior in complex mazes.Provides software MATLAB package for linearization of place fields in complex mazes. | Place fields linearization, complex mazes, producing linear place fields, hippocampal cells, complex mazes behavior, OpenBehavior |
is listed by: OpenBehavior is related to: LinCoM |
DOI:10.1101/2020.08.17.253849 | Free, Freely available | SCR_021438 | SciCrunch Registry | LinCoM | 2026-10-31 12:19:26 | 0 | ||||||||
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EthoWatcher project Resource Report Resource Website |
EthoWatcher project (RRID:SCR_021435) | data or information resource, portal, project portal | Project related to video tracking, detailed ethography, and extraction of kinematic variables from digital video files of laboratory animals.Provides computational tool developed at Federal University of Santa Catarina. | Video tracking, kinematic variables extraction. digital video files, laboratory animals, OpenBehavior |
is listed by: OpenBehavior is related to: EthoWatcher has parent organization: Federal University of Santa Catarina; Santa Catarina; Brazil |
DOI:10.1016/j.compbiomed.2011.12.002 | Free, Freely available | SCR_021435 | SciCrunch Registry | EthoWatcher | 2026-10-31 12:19:28 | 0 | ||||||||
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Automated Rodent Tracker project Resource Report Resource Website |
Automated Rodent Tracker project (RRID:SCR_021432) | ART | data or information resource, portal, project portal | Project related to development of automated rodent tracking position and movement. Provides software tool to automatically track rodent.Used to track head movements, body movements and also aspects of body size.Identifies certain behaviours from video footage, such as rotations, moving forwards, interacting with objects and staying still. | Track rodent position, track movement, track head movements, track body movements, OpenBehavior |
is listed by: OpenBehavior is related to: Automated Rodent Tracker |
DOI:10.1016/j.jneumeth.2017.04.006 | Free, Freely available | SCR_021432 | SciCrunch Registry | Automated Rodent Tracker | 2026-10-31 12:19:26 | 0 | |||||||
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DeepSqueak project Resource Report Resource Website |
DeepSqueak project (RRID:SCR_021450) | data or information resource, portal, project portal | Project related to rodent social communication through repertoire of ultrasonic vocalizations. Provides deep learning based system for quantification of Ultrasonic Vocalizations.Includes software MATLAB package for high throughput USV detection, classification, and analysis. | data quantification, ultrasonic vocalizations quantification, ultrasonic vocalization, OpenBehavior |
is listed by: OpenBehavior is related to: DeepSqueak |
DOI:10.1038/s41386-018-0303-6 | Free, Freely available | SCR_021450 | SciCrunch Registry | DeepSqueak | 2026-10-31 12:19:28 | 0 | ||||||||
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Camera Control project Resource Report Resource Website |
Camera Control project (RRID:SCR_021569) | data or information resource, portal, project portal, software resource | Portal provides Python based camera software GUI developed by Harvard University scientists. Open source software package that allows video to be recorded in sync with behavior. Python API to record video system timestamps from Imaging Source USB cameras. | Camera software, Python API, record video system timestamps, Imaging Source USB cameras, OpenBehavior |
is listed by: OpenBehavior is related to: Camera Control has parent organization: Harvard University; Cambridge; United States |
Free, Freely available | SCR_021569 | SciCrunch Registry | Camera Control | 2026-10-31 12:19:27 | 0 | |||||||||
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Rigbox project Resource Report Resource Website |
Rigbox project (RRID:SCR_021444) | data or information resource, portal, project portal | Project related to streamlining behavioral neuroscience experiments.Provides open source software MATLAB toolbox for running behavioral neuroscience experiments and managing data.Used for probing neurons and behavior. | Managing behavioral neuroscience experiments, running behavioral neuroscience experiments, managing data, acquiring experiment related data, OpenBehavior |
is listed by: OpenBehavior is related to: Rigbox |
DOI:10.1523/eneuro.0406-19.2020 | Free, Freely available | SCR_021444 | SciCrunch Registry | Rigbox | 2026-10-31 12:19:27 | 0 | ||||||||
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Online Animal Tracker project Resource Report Resource Website |
Online Animal Tracker project (RRID:SCR_021386) | OAT | data or information resource, portal, project portal | Project related to processing video, extracting object position information, and streaming data.Provides set of programs for processing video for behavioral research. Includes OAT software tool as real time position tracker which was developed by Massachusetts Institute of Technology scientists. | Real time animal position tracking, experimental neuroscience, real time object tracking, processing images, extracting object position information, streaming data to disk, OpenBehavior |
is listed by: OpenBehavior is related to: Online Animal Tracker has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Free, Freely available | SCR_021386 | SciCrunch Registry | Online Animal Tracker | 2026-10-31 12:19:26 | 0 | ||||||||
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Behavioral Segmentation of Open-field in DeepLabCut project Resource Report Resource Website |
Behavioral Segmentation of Open-field in DeepLabCut project (RRID:SCR_021410) | B-SOiD | data or information resource, portal, project portal | Project related to unsupervised behavior analysis.Carnegie Mellon University has shared B-SOiD, open source unsupervised algorithm for discovery of spontaneous behaviors. Includes software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users. | OpenBehavior, pairs unsupervised pattern recognition, supervised classification, behavior predictions, discovers actions, classifies actions |
is listed by: OpenBehavior is related to: Behavioral Segmentation of Open-field in DeepLabCut has parent organization: Carnegie Mellon University; Pennsylvania; USA |
DOI:10.1101/770271 | Free, Freely available | SCR_021410 | SciCrunch Registry | B-SOiD v2.0, Behavioral Segmentation of Open-field in DeepLabCut | 2026-10-31 12:19:26 | 0 | |||||||
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Simple Behavior Analysis project Resource Report Resource Website |
Simple Behavior Analysis project (RRID:SCR_021411) | data or information resource, portal, project portal | University of Washington project SimBA for analysis of complex social behaviors.Used for automated behavioral scoring. Includes open source software toolkit for computer classification of complex social behaviors in experimental animals. Uses data from popular open source tracking tools in combination with small amount of behavioral annotations to create supervised machine learning classifiers that can then rapidly and accurately score behaviors across different background settings and lighting conditions. | Complex social behaviors classifications, supervised behavioral classifiers development, score behaviors across different background settings, OpenBehavior |
is listed by: OpenBehavior is related to: Simple Behavior Analysis has parent organization: University of Washington; Seattle; USA |
DOI:10.1101/2020.04.19.049452 | Free, Freely available | SCR_021411 | SciCrunch Registry | Simple Behavior Analysis, SimBA | 2026-10-31 12:19:27 | 0 |
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